Contacts of the helix formed by residues 606 - 617 (chain D) in PDB entry 3JW0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 606 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603D HIS* 3.1 10.3 + - + +
605D ASN* 1.3 82.4 + - - +
607D ILE* 1.3 66.6 + - - +
608D PHE* 3.2 3.9 + - - +
609D GLU* 3.5 20.4 + - - +
610D GLU* 3.1 42.8 + - - +
613D ARG* 3.8 11.6 + - - -
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Residues in contact with ILE 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602D LEU* 4.1 19.9 - - + +
603D HIS 3.3 7.9 + - - +
604D ARG* 4.0 15.7 - - - +
605D ASN 5.3 0.7 - - - -
606D ASN* 1.3 77.7 - - - +
608D PHE* 1.3 65.1 + - - +
610D GLU* 4.7 3.8 - - - -
611D SER* 3.0 27.7 + - - -
632D PHE* 4.5 3.8 - - + -
647D TRP* 3.8 29.8 - - + +
650D LEU* 3.6 40.4 - - + +
651D LEU* 4.2 9.6 - - + +
654D GLU* 3.9 26.9 - - + +
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Residues in contact with PHE 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D ASN 3.2 1.2 + - - -
607D ILE* 1.3 81.5 - - - +
609D GLU* 1.3 82.2 + - + +
611D SER* 2.6 21.2 + - - -
612D TYR* 2.9 15.2 + - - +
651D LEU* 4.0 17.9 - - + -
654D GLU* 3.9 24.0 - - + +
655D MET* 3.9 20.0 - - + -
660D TYR* 3.2 46.7 - + - +
662D LEU* 4.3 14.6 - - + -
689D TYR* 3.9 27.8 - + - -
692D PHE* 3.7 20.6 - + - -
693D ILE* 4.6 0.7 - - + -
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Residues in contact with GLU 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D ASN* 3.5 24.2 + - - +
608D PHE* 1.3 100.2 - - + +
610D GLU* 1.3 57.8 + - - +
612D TYR* 3.4 11.5 - - - +
613D ARG* 3.0 60.7 + - - +
660D TYR* 5.0 2.8 - - + -
689D TYR* 3.1 28.6 + - - -
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Residues in contact with GLU 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600D MET* 5.1 0.9 - - - -
601D LYS 4.8 3.3 - - - +
602D LEU* 3.5 17.2 - - + +
603D HIS* 2.6 64.2 + - - +
606D ASN* 3.1 32.3 + - - +
607D ILE 4.3 0.4 - - - +
609D GLU* 1.3 73.7 - - - +
611D SER* 1.3 66.8 + - - +
613D ARG* 3.3 15.7 + - - +
614D ARG* 2.9 24.5 + - - +
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Residues in contact with SER 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600D MET* 3.7 23.8 - - - -
602D LEU* 4.8 1.7 - - - +
607D ILE 3.0 16.7 + - - -
608D PHE 2.6 19.8 + - - -
610D GLU* 1.3 73.4 - - - +
612D TYR* 1.3 72.8 + - - +
614D ARG 3.3 0.3 + - - -
615D ILE* 2.9 26.3 + - - +
647D TRP* 4.1 6.7 - - - -
651D LEU* 3.5 26.3 - - - +
692D PHE* 3.3 15.4 - - - -
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Residues in contact with TYR 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D PHE* 2.9 12.8 + - + +
609D GLU* 3.4 18.2 - - - +
611D SER* 1.3 85.5 + - - +
613D ARG* 1.3 83.1 + - + +
616D MET* 2.9 56.9 + - + +
685D ASP* 5.4 2.3 - - - +
688D SER* 2.8 27.8 + - - -
689D TYR* 3.6 48.9 - + + -
692D PHE* 3.8 26.0 - + + -
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Residues in contact with ARG 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D ASN* 3.8 21.0 + - - -
609D GLU* 3.0 50.2 + - - +
610D GLU* 3.3 12.9 + - - +
612D TYR* 1.3 91.7 - - + +
614D ARG* 1.3 53.4 + - - +
616D MET* 5.1 1.3 - - - -
617D SER* 2.6 36.3 + - - -
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Residues in contact with ARG 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598D PHE* 3.0 47.3 - - + -
599D GLU* 2.6 36.8 + - - +
600D MET* 4.0 20.9 - - + +
601D LYS 5.9 0.4 - - - +
610D GLU 2.9 20.2 + - - +
611D SER 3.8 2.0 - - - +
613D ARG* 1.3 71.6 - - - +
615D ILE* 1.3 63.3 + - - +
617D SER* 2.8 22.4 + - - -
618D VAL* 3.6 10.7 + - - +
619D LYS* 3.5 25.3 + - - +
623D VAL* 5.7 0.2 - - - +
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Residues in contact with ILE 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598D PHE* 3.6 16.4 - - + -
600D MET* 4.3 17.0 - - + -
611D SER 2.9 18.7 + - - +
614D ARG* 1.3 76.5 - - - +
616D MET* 1.3 63.6 + - - +
618D VAL* 3.1 25.1 - - - +
624D LEU* 3.5 27.1 - - + -
628D LEU* 6.2 0.2 - - + -
647D TRP* 4.6 7.6 - - + -
692D PHE* 3.9 23.1 - - + -
695D ARG* 3.9 30.0 + - + -
696D VAL* 5.3 1.8 - - + -
699D LEU* 4.0 17.9 - - + -
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Residues in contact with MET 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D TYR* 2.9 53.3 + - + +
613D ARG* 4.5 1.3 - - - +
615D ILE* 1.3 70.0 - - - +
617D SER* 1.3 59.0 + - - +
618D VAL 2.9 16.8 + - - +
688D SER* 3.6 32.8 - - - +
691D THR* 4.0 14.1 - - + -
692D PHE* 4.0 20.0 - - + -
695D ARG* 3.5 38.3 + - - +
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Residues in contact with SER 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D ARG 2.6 23.7 + - - -
614D ARG* 2.8 15.4 + - - -
616D MET* 1.3 75.2 - - - +
618D VAL* 1.3 64.2 + - - +
619D LYS* 3.4 13.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il